comparison autogenJB2.py @ 71:e26a8a6d2d2e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cf208cecf0140ff43d145a44713ab7108057fb8b

70:5f0ee87daef4

                        },
                    }
                    for i, x in enumerate(genome_paths)
                ],
            )
            logging.warn("#!!! paths=%s, genomes=%s" % (genome_paths, genomes))
            assref_name = jc.process_genomes(genomes[0])
            default_session_data = {
                "visibility": {
                    "default_on": [],
                    "default_off": [],

            # }
            jc.add_general_configuration({})
            trackconf = jc.config_json.get("tracks", [])
            for gnome in jc.genome_names:
                trackconf += jc.tracksToAdd[gnome]
            logging.warn(
                "++++ adding trackconf=%s for gnome %s" % (trackconf, gnome)
            )
            jc.config_json["tracks"] = trackconf
            assconf = jc.config_json.get("assemblies", [])
            assconf += jc.assemblies
            jc.config_json["assemblies"] = assconf
            logging.warn("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
            jc.write_config()
            default_session_data.update({"session_name": sessName})
            track_conf.update(default_session_data)
            jc.add_default_session(default_session_data)
            # jc.text_index() not sure what broke here.

71:e26a8a6d2d2e

                        },
                    }
                    for i, x in enumerate(genome_paths)
                ],
            )
            logging.debug("#!!! paths=%s, genomes=%s" % (genome_paths, genomes))
            assref_name = jc.process_genomes(genomes[0])
            default_session_data = {
                "visibility": {
                    "default_on": [],
                    "default_off": [],

            # }
            jc.add_general_configuration({})
            trackconf = jc.config_json.get("tracks", [])
            for gnome in jc.genome_names:
                trackconf += jc.tracksToAdd[gnome]
            logging.debug(
                "++++ adding trackconf=%s for gnome %s" % (trackconf, gnome)
            )
            jc.config_json["tracks"] = trackconf
            assconf = jc.config_json.get("assemblies", [])
            assconf += jc.assemblies
            jc.config_json["assemblies"] = assconf
            logging.debug("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
            jc.write_config()
            default_session_data.update({"session_name": sessName})
            track_conf.update(default_session_data)
            jc.add_default_session(default_session_data)
            # jc.text_index() not sure what broke here.